Cloning & PCR

LECTURE 4:

Biotechnology; 3 Credit hours

Atta-ur-Rahman School of Applied Biosciences (ASAB)National University of Sciences and Technology (NUST)

Polymerase Chain Reaction

• Polymerase: DNA polymerase– DNA polymerase duplicates DNA– Before a cell divides, its DNA must be

duplicated• Chain Reaction: The product of a reaction

is used to amplify the same reaction – Results in rapid increase in the product

Polymerase Chain Reaction (PCR)

• PCR performs the chemistry of DNA duplication in vitro

• Numerous PCR applications make this process a staple in most biology laboratories

• Understanding properties of DNA polymerases helps understanding PCR

Discovery• PCR was discovered by Kary Mullis– On a long motorcycle drive– According to Mullis, he was driving his vehicle late night with his

girlfriend– Mentally visualized the process

• Nobel Prize in Chemistry– 1993

DNA polymerase

• Duplicates DNA• Necessary for reproduction of new cells• More than one DNA polymerases exist in

different organisms

Properties of DNA polymearse

3’ 5’

5’ 3’

• Needs a pre-existing DNA to duplicate– Cannot assemble a new strand from

components– Called template DNA

• Can only extend an existing piece of DNA– Called primers

Properties of DNA polymearse

• DNA strands are anti-parallel– One strand goes in 5’ 3’– The complementary strand is opposite

• DNA polymerase always moves in one direction (from 5’ 3’)

3’ 5’

5’ 3’

Properties of DNA polymearse

• DNA polymerase incorporates the four nucleotides (A, T, G, C) to the growing chain

• dNTP follow standard base pairing rule

3’ 5’

5’ 3’

dCTP

dTTP

dCTPdGTPdATP

dGTP

dCTP

dTTP

dATP

dGTP

dCTP

dTTP

dATP

dATP

dGTPdCTP dTTPdATP dGTP

dATP

dGTP

dTTP

dATP

dCTP

dTTP

Properties of DNA polymearse

• The newly generated DNA strands serve as template DNA for the next cycle

• PCR is very sensitive• Widely used

Setting up a PCR Reaction

• Add template DNA and primers• Add dNTPs• Add DNA polymerase

3’ 5’

5’ 3’

dCTP

dTTP

dCTPdGTPdATP

dGTP

dCTP

dTTP

dATP

dGTP

dCTP

dTTP

dATP

dATP

dGTPdCTP dTTPdATP dGTP

dATP

dGTP

dTTP

dATP

dCTP

dTTP

Properties of DNA polymearse

• DNA polymerase needs Mg++ as cofactor• Each DNA polymerase works best under

optimal temperature, pH and salt concentration

• PCR buffer provides optimal pH and salt condition

Taq DNA polymerase

• Derived from Thermus aquaticus• Heat stable DNA polymerase• Ideal temperature 72C

Thermal Cycling

• A PCR machine controls temperature• Typical PCR go through three steps–Denaturation–Annealing– Extension

Denaturation

• Heating separates the double stranded DNA– Denaturation

• Slow cooling anneals the two strands– Renaturation

Heat Cool

Annealing

• Two primers are supplied in molar excess

• They bind to the complementary region

• As the DNA cools, they wedge between two template strands

• Optimal temperature varies based on primer length etc.

• Typical temperature from 40 to 60 C

Extension

• DNA polymerase duplicates DNA• Optimal temperature 72OC

PCR Amplification

Exponential Amplification of template DNA

Typical PCR mix

In a thin wall Eppendorf tube assemble the following

PCR components Amount

Template DNA (5-200 ng)1 mM dNTPs (200 uM final)10 X PCR buffer25 mM MgCl2 (1.5 mM final)20 uM forward primer (20 pmoles final)20 uM reverse primer (20 pmoles final)5 units/uL Taq DNA polymerase (1.5 units)WaterFinal Volume

variable10 uL5 uL3 uL1 uL1 uL0.3 uLVariable50 uL

Applications

• Revolutionized how we study biology– Recombinant DNA Technology– Research– Diagnostics– Forensics